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There's also Lean for proof assistance.
Add THREE.js for topology/geometry visualizations and Sage for symbolic computation
Totally agree. I would add that Pluto.jl is an excellent platform for studying, prototyping and exploring concepts in general.
Making that better is an open problem in the proof assistant community. It is being actively worked on. The main project I know of that's working on this in the context of pure math is Project Xena, which focuses on the Lean proof assistant/programming language. You might find that project interesting and useful. I think it is likely that this situation will improve over the next few years, but probably not sooner than that.
As a Rust book, I would just use the Rust book, https://doc.rust-lang.org/book/. But of course in most cases using Rust is a total overkill (not in my area though).